CAGEcleaner
===================

main
-----------------------

.. automodule:: cagecleaner.main
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   :undoc-members:
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run
----------------------

.. automodule:: cagecleaner.run
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   :undoc-members:
   :show-inheritance:

genome\_run
-----------

.. automodule:: cagecleaner.genome_run
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   :undoc-members:
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local\_genome\_run
-------------------

.. automodule:: cagecleaner.local_genome_run
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   :undoc-members:
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local\_region\_run 
-------------------------------------

.. automodule:: cagecleaner.local_region_run
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   :undoc-members:
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local\_run
-----------------------------

.. automodule:: cagecleaner.local_run
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   :undoc-members:
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region\_run
------------------------------

.. automodule:: cagecleaner.region_run
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   :undoc-members:
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remote\_genome\_run
--------------------------------------

.. automodule:: cagecleaner.remote_genome_run
   :members:
   :undoc-members:
   :show-inheritance:

remote\_region\_run
--------------------------------------

.. automodule:: cagecleaner.remote_region_run
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   :undoc-members:
   :show-inheritance:

remote\_run
------------------------------

.. automodule:: cagecleaner.remote_run
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   :undoc-members:
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communication
-------------

.. automodule:: cagecleaner.communication
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   :undoc-members:
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file\_utils
------------

.. automodule:: cagecleaner.file_utils
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   :undoc-members:
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utils
------------------------

.. automodule:: cagecleaner.utils
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   :undoc-members:
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